Implementation Analysis : Cell Morphological Enrichment Analysis

At it’s heart, “Cell One” is a coming of age story about a young man learning to value mature, fair, nonviolent behavior as a form of communication and order as a way of life. Nnamabia has lived his entire life in a culture where vicious boys are the most popular, both in their Nigerian town and seemingly in American rap videos where gangs and other illegal behavior is regarded as a path to living a life full of fame and wealth. Being a typical adolescent boy, Nnamabia wants to seem like he’s part of the “in crowd” of the college campus and tries to make it seem like he is doing all the crime without actually taking on any risk. Once he is confronted with the consequences of his actions and kept in the corrupt prison, he realizes that the way he has been acting will get him killed or worse.

The Basic Local Alignment Search Tool (BLAST) was the final portion of this lab report. BLAST is provided courtesy of the National Center for Biotechnology Information (NCBI). After running the five chosen tests, students were given the two 16S rRNA sequences that were associated with their assigned culture. The BLAST results served to confirm or disprove the hypothesis of what the unknown may be. The BLAST program compared the given 16S rRNA sequence to a database of known sequences and searched for similarity. (10) This search tool is capable of comparing nucleotide or protein sequences to find statistical significance between the matches. A perfect match to the unknown sequence is indicated by a

In the first lab exercise, an introduction and tasks were performed to study the CDK2 (1hcl). To perform this exercise a PDB file of protein was downloaded and analysed under different representations. Each representation depicted different configuration such as WIREFRAME, SPACEFILL, BACKBONE, RIBBONS, BALL AND STICK, CARTOONS, STRANDS and MOLECULAR SURFACE format. All these representations were retrieved from computer based program software called Raswin/Rasmol. RasMol was originally developed by its interactive, free molecular-graphics viewer originally developed by Roger Sayle (http://www.openrasmol.org/).This program reads the molecule in the 3-D coordination using the pdb file format (https://en.wikipedia.org/wiki/RasMol). The molecules are displayed in different formats and permits one to rotate the molecule interactively, allowing view of multiple molecules (https://en.wikipedia.org/wiki/RasMol). In the second lab exercise, domain annotations based

Introduction The purpose of this lab was to study cell physiology. This is described as the scientific procedure that studies the functions of cells growth and their maintenance, self-regulation, their divisions and interactions. This involve their functions through the nucleus, cytoplasm, and general behavior of protoplasm. Physiology is the science that analyzes the functionality of living organisms, its structures, and the chemical and physical aspects involve in it. While people analyze cells components, they can notice the development of cells and how they get untied to form organs and other structures.

Good morning. This is Larry Lysosome here. I work at The Cell Corporation. My job here at Cell Co. is to recycle the other malfunctioning parts of the cell and return their nutrients back into the cell. I write to you because I am aware that you will soon be firing some employees here at Cell Co. and wanted to inform you that Cell Co. would be a complete mess without me (no pun intended). I'm a vital part of the corporation and it would be nearly impossible for the other organelles as well as you Mrs.Eukaryote to work properly without me. So I ask that you take a moment to listen to me and consider what I have to say.

By using the ligation mixture formed in experiment 3B, competent cells undergo transformation in this experiment. The cells do not usually exist in a state of transformation ready but they can be made permeable to the plasmid DNA and the capable of transformation are referred as competent. Transformation is the uptake of heritable information in a competent cell. Competent cells care extremely fragile and need to be handle gently to ensure the success of transformation. Water bath is heated to 42oC as heat shock treatment to start transformation. The competent cells containing recombinant vectors can be identified through blue white screening. Cells containing recombinant vectors are able to survive on Luria Bertani (LB) medium supplemented with the antibiotic, penicillin. The cells transformed by recombinant vectors are plating on plate that containing isopropyl β-D-thiogalactopyranoside (IPTG) which as an inducer of the lac promoter, and 5-bromo-4-chloro-3-indolyl- β-D-galactoside or called X-Gal which is a dye that produces a blue colour when

Each cell in our body is composed of the same DNA, yet different cells synthesize different proteins. In other words, each cell has the same genotype, but different phenotypes. For example, our pancreatic beta cells make insulin and our epithelial cells make collagen. Why can our pancreatic beta cells not make collagen and our epithelial cells make insulin? This is all due to gene expression. Each cell is composed of every single gene, but only a certain collection is expressed. The regulation of gene expression is more complex in eukaryotes, than prokaryotes. This essay will discuss both and how key steps and possible decisions influence which cell has which phenotype.

Working as a Research Assistant at the Piano Laboratory, I have an interest in developmental biology. At the Piano Lab, I assist my mentor, Patricia Giselle Cipriani, and her project on the usage of RNAi on ovary-expressed genes and of time-lapse microscopy in order to better understand a comprehensive molecular description of the genetic and evolutionary mechanisms behind early embryogenesis in C. elegans. From the data obtained from the RNAi tests, gene clusters based on the phenotypic analysis are created in order to investigate the functional analysis of the genome and molecular dissection of specific cellular processes. My role in the laboratory is to identify and verify the locations of single polymorphisms in mutants and then perform gel electrophoresis to verify mutations before sequencing. In the process, I also learned basic microscopy and worm-handling skills.

**Annotated Figures 1-5 were sourced and calculated from the cumulative results of the BIOL2029: Cells, Wednesday lab section**

The decision of NSCs to either stay in the pool of proliferating, undifferentiated cells or to differentiate is dictated by extracellular and intracellular factors that are affected by the cell cycle mechanism.

We also assume that the number of initial cell population in a treated condition is the same as one in an untreated control condition. Then cell viability is written as a function of growth rates and time. We consider the same time scale of our cell viability assay in our experiments.Here, we defined tumor and stroma region explicitly based on an image of lung adenocarcinoma patient tissue. Tumor region contains cancer cells. Since not all proteins in cancer cells are directly measurable due to experimental limitation, many players and intermediate proteins in the pathway are not included in our study. For this reason, an interaction between two proteins is not necessarily representing direct interaction. Rather, it represents diverse and abstract influence of one entity to other entity in steady state, where an entity can be a microenvironmental variable, intracellular protein, or cell viability.

[3] T. Tengs et al, "Microarray-based method for detection of unknown genetic modifications," BMC Biotechnology, vol. 7, (1), pp. 91, 2007. Available: http://www.ncbi.nlm.nih.gov/pubmed/18088429. DOI: 10.1186/1472-6750-7-91.

\textit{CellProfiler} software was applied to process images and calculate samples aggregation for features in response to a compound treatment \cite{40}.

In Chapter 4, I aimed to elucidate the effect of A83-01 by targeting TGF-R signalling, given that TGF-β is a pleiotropic cytokine with multifunctional roles in cells (Massague, 2012). Based on RNA seq gene expression profiling of A83-01-treated and control eMSC, this study has provided vast information on the role of the numerous signalling pathways and their crosstalk. By comparing the profile I obtained from A83-01 treated and untreated eMSCs with a gene signature generated from freshly isolated eMSCs and fibroblast profile of cultured eMSCs with that from Barragan et al verified a common gene signature of fibroblasts (Barragan et al., 2016), confirming the rescue of eMSCs spontaneous differentiation in cultures by A83-01. Many genes

To solve Q1 and Q3 in Figure 1, we evaluated the performance of each tool in a variety of genes associated with lysosomal diseases. To evaluate the false negative rate of each tool, we submitted all 385 known disease-associated missense mutations of IDUA, IDS and GLB1 genes into these tools. Significant concordance was observed between the functional consequences of missense mutations predicted by various combinations of the tools. Out of 385 known disease-causing mutations, 155 (40.3%) were predicted to be ‘damaging’ by all 7 tools and 197 (51.2%) were predicted to be ‘damaging’ by at least 6 tools. As shown in Figure 2, PROVEAN and PolyPhen turned out to be the most